I know variants of this have been answered a few times, but thus far I've had no luck: I'm attempting to install Rgraphviz from bioconductor. I downloaded the stablemac version from http://www.graphviz.org/Download_macos.php and used biocite to install Rgraphviz after installing bioconductor. However, when I attempt to load Rgraphviz, I get the following error. Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Users/jbyr/Library/R/2.9/library/ Rgraphviz/libs/ppc/Rgraphviz.so': dlopen(/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/ Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib Referenced from: /Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ ppc/Rgraphviz.so Reason: image not found Error: package/namespace load failed for 'Rgraphviz' I went to look for libgvc.3.dylib, and there in /usr/lib found libgvc. 5.dylib . Is the answer here to install an older version of graphviz? If so which one? Or can Rgraphviz be made to work with my existing installation of graphviz? -Jarrett
installing Rgraphviz
3 messages · Jarrett Byrnes, Patrick Aboyoun
Jarrett, This is a Bioconductor related question and really should be addressed on the Bioconductor mailing list. The sort answer is if you are running on a Mac OS X 10.4 (Tiger) box, you will need to build both graphviz and Rgraphviz from source in order to use the package. If you are running on a Mac OS X 10.5 (Tiger) box, continue reading. The issue is that graphviz.org distributes their latest version of Graphviz for Mac OS X 10.5 (Leopard) only and we use that when we build our mac.binary.leopard version of Rgraphviz. I am guessing that you are using the cross Mac OS X pre-compiled version of R, which uses the mac.binary build of the package from our Mac OS X 10.4 (Tiger) build machine that has an old (unmaintained) version of graphviz on it. I recommend that all Bioconductor users running on leopard to use a leopard-only build of R available at http://r.research.att.com/, since that is what we use on our build machine. These leopard only R binaries download, via biocLite, mac.binary.leopard versions of the packages that are produced by our Leopard machine. These leopard only binaries have the added benefit of 64-bit Intel support so end-users don't have to build their own packages once they leave the 32-bit world. Patrick
Jarrett Byrnes wrote:
I know variants of this have been answered a few times, but thus far I've had no luck: I'm attempting to install Rgraphviz from bioconductor. I downloaded the stablemac version from http://www.graphviz.org/Download_macos.php and used biocite to install Rgraphviz after installing bioconductor. However, when I attempt to load Rgraphviz, I get the following error. Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so': dlopen(/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib Referenced from: /Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so Reason: image not found Error: package/namespace load failed for 'Rgraphviz' I went to look for libgvc.3.dylib, and there in /usr/lib found libgvc.5.dylib . Is the answer here to install an older version of graphviz? If so which one? Or can Rgraphviz be made to work with my existing installation of graphviz? -Jarrett
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Typo. Change Mac OS X 10.5 (Tiger) to Mac OS X 10.5 (Leopard) below.
Patrick Aboyoun wrote:
Jarrett, This is a Bioconductor related question and really should be addressed on the Bioconductor mailing list. The sort answer is if you are running on a Mac OS X 10.4 (Tiger) box, you will need to build both graphviz and Rgraphviz from source in order to use the package. If you are running on a Mac OS X 10.5 (Tiger) box, continue reading. The issue is that graphviz.org distributes their latest version of Graphviz for Mac OS X 10.5 (Leopard) only and we use that when we build our mac.binary.leopard version of Rgraphviz. I am guessing that you are using the cross Mac OS X pre-compiled version of R, which uses the mac.binary build of the package from our Mac OS X 10.4 (Tiger) build machine that has an old (unmaintained) version of graphviz on it. I recommend that all Bioconductor users running on leopard to use a leopard-only build of R available at http://r.research.att.com/, since that is what we use on our build machine. These leopard only R binaries download, via biocLite, mac.binary.leopard versions of the packages that are produced by our Leopard machine. These leopard only binaries have the added benefit of 64-bit Intel support so end-users don't have to build their own packages once they leave the 32-bit world. Patrick Jarrett Byrnes wrote:
I know variants of this have been answered a few times, but thus far I've had no luck: I'm attempting to install Rgraphviz from bioconductor. I downloaded the stablemac version from http://www.graphviz.org/Download_macos.php and used biocite to install Rgraphviz after installing bioconductor. However, when I attempt to load Rgraphviz, I get the following error. Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so': dlopen(/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib Referenced from: /Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so Reason: image not found Error: package/namespace load failed for 'Rgraphviz' I went to look for libgvc.3.dylib, and there in /usr/lib found libgvc.5.dylib . Is the answer here to install an older version of graphviz? If so which one? Or can Rgraphviz be made to work with my existing installation of graphviz? -Jarrett
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